In article <9209291857.AA05863 at genbank.bio.net>, ANMR1 at UORDB2.bitnet writes:
|> I would like to find out how to use the Lander MAPMAKER program to
|> analyze F2 intercross data for mapping when the homozygous recessive
|> for one marker is partially lethal. For example, when that marker gives a
|>|> distorted Mendelian ratio of (say) 7:1 in F2, instead of 3:1, due to partial
|> embryo lethality. I would appreciate if someone comments on this.
|> Thanks.
|> Animesh Ray
The first thing you should try is a chi square test for independence to test for associations between markers and the trait. You cannot do this in mapMaker but it is possible to do it in a spread sheet program. If you have a large F2 population, and the molecular markers that you are testing for linkage do not exhibit a distorted segregation ratio, then you can analyse the data for linkage in mapmaker. The linkage estimate will have a higher variance than normal, but you will know the general location of
the lethal.